rs5873543

Variant names:

• chr5-176626335-GGTGTGTGTGTGT-G
• rs5873543
• NM_003085.5:c.282+51_282+62delACACACACACAC

Your query was ambiguous. Multiple possible variants found:

• chr5-176626335-GGTGTGTGTGTGT-G
• chr5-176626335-GGTGTGTGTGTGT-GGT
• chr5-176626335-GGTGTGTGTGTGT-GGTGT
• chr5-176626335-GGTGTGTGTGTGT-GGTGTGT
• chr5-176626335-GGTGTGTGTGTGT-GGTGTGTGT
• chr5-176626335-GGTGTGTGTGTGT-GGTGTGTGTGT
• chr5-176626335-GGTGTGTGTGTGT-GGTGTGTGTGTGTGT
• chr5-176626335-GGTGTGTGTGTGT-GGTGTGTGTGTGTGTGT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_003085.5(SNCB):​c.282+51_282+62delACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000444 in 864,318 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00025 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00048 (2 hom.)
• Consequence: SNCB NM_003085.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.15

Genes affected

SNCB (HGNC:11140): (synuclein beta) This gene encodes a member of a small family of proteins that inhibit phospholipase D2 and may function in neuronal plasticity. The encoded protein is abundant in lesions of patients with Alzheimer disease. A mutation in this gene was found in individuals with dementia with Lewy bodies. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 38 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNCB	NM_003085.5	c.282+51_282+62delACACACACACAC		intron_variant	Intron 4 of 5	ENST00000393693.7	NP_003076.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNCB	ENST00000393693.7	c.282+51_282+62delACACACACACAC		intron_variant	Intron 4 of 5	1	NM_003085.5	ENSP00000377296.2

Frequencies

GnomAD3 genomes AF: 0.000261 AC: 39 AN: 149346 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000582

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00554

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000163

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000484 AC: 346 AN: 714868 Hom.: 2 AF XY: 0.000702 AC XY: 269 AN XY: 383278

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000232

Gnomad4 ASJ exome AF: 0.0000949

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00397

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000885

Gnomad4 OTH exome AF: 0.000536

GnomAD4 genome AF: 0.000254 AC: 38 AN: 149450 Hom.: 0 Cov.: 0 AF XY: 0.000316 AC XY: 23 AN XY: 72892

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.000582

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00533

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000163

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5873543; hg19: chr5-176053336;